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1 // ***************************************************************************
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2 // BamWriter.cpp (c) 2009 Michael Str�mberg, Derek Barnett
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3 // Marth Lab, Department of Biology, Boston College
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4 // All rights reserved.
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5 // ---------------------------------------------------------------------------
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6 // Last modified: 4 March 2011 (DB)
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7 // ---------------------------------------------------------------------------
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8 // Provides the basic functionality for producing BAM files
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9 // ***************************************************************************
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10
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11 #include <api/BamAlignment.h>
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12 #include <api/BamWriter.h>
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13 #include <api/SamHeader.h>
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14 #include <api/internal/BamWriter_p.h>
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15 using namespace BamTools;
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16 using namespace BamTools::Internal;
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17
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18 #include <iostream>
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19 using namespace std;
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20
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21 /*! \class BamTools::BamWriter
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22 \brief Provides write access for generating BAM files.
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23 */
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24 /*! \enum BamTools::BamWriter::CompressionMode
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25 \brief This enum describes the compression behaviors for output BAM files.
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26 */
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27 /*! \var BamWriter::CompressionMode BamWriter::Compressed
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28 \brief Use normal BAM compression
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29 */
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30 /*! \var BamWriter::CompressionMode BamWriter::Uncompressed
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31 \brief Disable BAM compression
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32
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33 Useful in situations where the BAM data is streamed (e.g. piping).
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34 It would be wasteful to compress, and then immediately decompress
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35 the data.
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36 */
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37
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38 /*! \fn BamWriter::BamWriter(void)
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39 \brief constructor
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40 */
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41 BamWriter::BamWriter(void)
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42 : d(new BamWriterPrivate)
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43 { }
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44
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45 /*! \fn BamWriter::~BamWriter(void)
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46 \brief destructor
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47 */
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48 BamWriter::~BamWriter(void) {
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49 delete d;
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50 d = 0;
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51 }
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52
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53 /*! \fn BamWriter::Close(void)
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54 \brief Closes the current BAM file.
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55 \sa Open()
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56 */
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57 void BamWriter::Close(void) {
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58 d->Close();
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59 }
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60
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61 /*! \fn bool BamWriter::IsOpen(void) const
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62 \brief Returns \c true if BAM file is open for writing.
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63 \sa Open()
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64 */
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65 bool BamWriter::IsOpen(void) const {
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66 return d->IsOpen();
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67 }
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68
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69 /*! \fn bool BamWriter::Open(const std::string& filename,
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70 const std::string& samHeaderText,
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71 const RefVector& referenceSequences)
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72 \brief Opens a BAM file for writing.
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73
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74 Will overwrite the BAM file if it already exists.
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75
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76 \param filename name of output BAM file
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77 \param samHeaderText header data, as SAM-formatted string
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78 \param referenceSequences list of reference entries
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79
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80 \return \c true if opened successfully
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81 \sa Close(), IsOpen(), BamReader::GetHeaderText(), BamReader::GetReferenceData()
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82 */
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83 bool BamWriter::Open(const std::string& filename,
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84 const std::string& samHeaderText,
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85 const RefVector& referenceSequences)
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86 {
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87 return d->Open(filename, samHeaderText, referenceSequences);
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88 }
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89
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90 /*! \fn bool BamWriter::Open(const std::string& filename,
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91 const SamHeader& samHeader,
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92 const RefVector& referenceSequences)
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93 \brief Opens a BAM file for writing.
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94
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95 This is an overloaded function.
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96
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97 Will overwrite the BAM file if it already exists.
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98
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99 \param filename name of output BAM file
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100 \param samHeader header data, wrapped in SamHeader object
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101 \param referenceSequences list of reference entries
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102
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103 \return \c true if opened successfully
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104 \sa Close(), IsOpen(), BamReader::GetHeader(), BamReader::GetReferenceData()
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105 */
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106 bool BamWriter::Open(const std::string& filename,
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107 const SamHeader& samHeader,
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108 const RefVector& referenceSequences)
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109 {
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110 return d->Open(filename, samHeader.ToString(), referenceSequences);
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111 }
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112
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113 /*! \fn void BamWriter::SaveAlignment(const BamAlignment& alignment)
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114 \brief Saves an alignment to the BAM file.
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115
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116 \param alignment BamAlignment record to save
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117 \sa BamReader::GetNextAlignment(), BamReader::GetNextAlignmentCore()
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118 */
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119 void BamWriter::SaveAlignment(const BamAlignment& alignment) {
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120 d->SaveAlignment(alignment);
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121 }
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122
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123 /*! \fn void BamWriter::SetCompressionMode(const CompressionMode& compressionMode)
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124 \brief Sets the output compression mode.
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125
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126 Default mode is BamWriter::Compressed.
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127
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128 N.B. - Changing the compression mode is disabled on open files (i.e. the request will be ignored).
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129 Be sure to call this function before opening the BAM file.
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130
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131 \code
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132 BamWriter writer;
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133 writer.SetCompressionMode(BamWriter::Uncompressed);
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134 writer.Open( ... );
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135 // ...
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136 \endcode
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137
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138 \param compressionMode desired output compression behavior
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139 \sa IsOpen(), Open()
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140 */
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141 void BamWriter::SetCompressionMode(const CompressionMode& compressionMode) {
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142 d->SetWriteCompressed( compressionMode == BamWriter::Compressed );
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143 }
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